Skin Deep
by The Funtime Writer
Summary: Follow Lily Donavihn, a skilled Pokemon Trainer, on her journey to bring down Team Rocket from the inside, working undercover as Giovanni's best spy! Meeting old friends and making new, she will stop at nothing to save Unova and everything else! OC story
1. Chapter 1

**Just a quick note before the story begins, the idea that trainers can see inside the Pokeballs to see their Pokémon was an idea I mainly derived from the manga.**

Giovanni sat at his desk, browsing over paperwork with little to no interest. Team Rocket's activity had been severely downplayed as of late, their operation to slowly conquer the Unova region going much slowly than he had thought possible. Sure, that idiot trio had stepped up their game, but they were still low on his list. Maybe he should send one of his more competent soldiers..?

His mindset was interrupted as his Persian, which had always been his faithful partner, stood up from its position at his side, slowly padding away. The leader's gaze followed the Pokémon until it came to rest on his visitor.

"Back from your mission, I see."

Standing against the back wall of his office was a black clad figure, a red pin in the shape of an R pinned to a black longsleeve . A pair of black shorts accompanied with a belt lined with five Pokéballs, the sixth hanging from her neck. To finish it off were a set of high flexible boots that went past the knees and a metal jetpack backpack. The long brown hair pulled back into a ponytail was the only characteristic he could see besides the lithe figure, the soldier's face obscured by a high-tech visor.

"I assume you succeeded?" He asked aloud, resting his hand on a clenched hand. The criminal merely nodded, briefly bending down to stroke his Persian's head. "Excellent. It's always nice when a plan goes through perfectly." He smirked, nodding his head in approval.

"Ahem."

He looked up to see the worker extend their hand, rubbing the tips of their fingers together. Giovanni gave a small chuckle. "You're awfully impatient today."

"Perhaps because I don't approve of robbing a Pokémon nursery. "

"Ah. Well dear, you're usually the most skilled at picking out the best Pokémon."

"Whatever. Where's my payment?" The brunette retorted, crossing their arms. Giovanni gave a defeated sigh, fishing a pouch out of his desk drawer and tossing it to the worker. He watched as they opened it, thumbing through the bills to count them. The worker finally gave a nod of approval and turned to leave.

"Hold on a moment, Lily."

Lily Donavihn stopped, turning to face her boss. "Yeah?" She asked semi-impatiently. This had been her last job for the next few days, and she was eager to leave the base. She and her Pokemon both deserved a break.

"As one of my best, I'm positive you're aware of our ongoing project in Unova."

The brunette nodded, taking a seat in front of his desk. "How could I forget? I was just there last week with those three idiots. They almost destroyed several days worth of surveillance and planning. Why do you even keep them around, Giovanni?"

The Team Rocket leader sighed, rubbing his temples. "They aren't completely incompetent. Besides, their loyalty and devotion to our cause make them willing to do whatever I ask of them, unlike you." Her boss interlaced his fingers. "And take off that visor. You're too beautiful to hide it."

"Whatever." Lily murmured, slipping the mask into her backpack. Blue eyes narrowed at the leader. "So where's this conversation going?"Giovanni gave a chuckle in response. "Well Donavihn, since you're always so successful…" His expression grew more serious. "- I'd like you to head to Unova to spearhead the operation."

Lily crossed her arms. "No."

Giovanni raised a brow. "And why not?"

"_Because_ after today, I'm off duty for at least a week. I don't feel like poking around like a rat."

The leader sighed, running a few fingers through his hair. "Lily, dear, I assure you you'll be well compensated. Besides, you're next job is in Unova anyways."

The brunette's ears perked up. "…Fine, but Aelita's too tired to fly me there and Poseidon's resting. I'll need transport."

"That's fine with me. I'll need you to leave within the hour, though. Say your goodbyes and whatnot and head to the heliport." At this, Lily got up from her chair, craning her neck. "Alright. I'll send a message upon arrival." With a nod as an answer from her boss, she gave the Persian a farewell smile before heading out the door.

"Yo Donavihn, nice work today!" A male co-worker praised as she walked by. "Don't forget that next time we battle, I'll be winning!" The blue eyed blonde grinned, a personal buddy of hers.

"Whatever you say, Jake. Heading to Unova, though, so it'd have to wait."

With a disappointed groan from her friend, she gave a wave of goodbye and continued to walk. The brunette held up the Pokéball hanging from the silver chain around her neck, then looking down to the five around her belt. "You hear that guys? We get to vacation in Unova."

The Pokémon in her hand smiled. "Hey, do you want to come out?" Lily asked, watching as her partner nodded back. "Alright, come out, Vincent." The brunette pointed the ball next to her, a red beam shooting out and diminishing to reveal her partner standing beside her, a blue-eyed Gardevoir, and her very first Pokémon. He wore a bowtie and cufflinks, much like one would wear with a suit. It gave him a sophisticated look, and also let people know it was a male Gardevoir.

He walked beside her as she made her way to a Pokémon Healing Machine that was sitting in a hallway outside the heliport. One by one she unclipped the rest of her team from off her belt and put them into the machine. Torque the Blaziken, Aelita the Dragonite, Ran Mao the Mienshao, Lucas the Luxray, and lastly, Poseidon, her gargantuan Gyrados.

"You all did great today. I'm sorry I have to drag you all through this." She apologized, her head hanging low. Vincent, who was slightly taller than she was, put a hand on her shoulder comfortingly. He knew it was for the money, not the crime. Her salary with Team Rocket severely dwarfed any other job she could get, and although it wasn't something she could be proud of, it did support her and her friends.

With a sigh, she grabbed them from the machine and put them back on her belt, finished. "Oh, you must be Lily." A Team Rocket member mused as she strolled up to him in the heliport. "Yeah. Are you the helicopter pilot?" She asked back, receiving a snicker. "Helicopter? As if! I fly the jets, sweetheart."

"Jets. In a heliport." Lily said aloud, her statement having a questioning edge. She watched as the uniformed man walked over to a control panel on the wall, hitting a few buttons. The brunette turned to see a wall on the far side of the heliport slowly rise upwards, revealing a long outcrop that served as a runway.

"Since when did we get jets?" Lily asked as she walked beside him to a sleek black jet, stepping inside the passenger inside after Vincent, who sat in the middle. "Helicopters are clunky and slow while planes aren't fast enough, not to mention bulky." The pilot answered, beginning to flip switches as he fired up the engine. "This baby should get you to Unova in an hour, maybe less."

"Where'd we get the funding for this?"

"Remember that heist a while back? Supposedly this hot chick bagged us a ton of cash."

"Ah." Lily smirked inwardly, realizing that the pilot didn't know that had been her. She gazed out the tinted window as the jet began to drive forward, its speed a crescendo as they flew down the runway and soaring into the air. The brunette found herself gazing out the window, love-struck as she looked out the window and down below. Flocks of Wingull were flying in the air, a pod of the massive Pokémon Wailord swimming below.

Lily looked over to her faithful Gardevoir with a smile. "Looks like this is going to be a fun trip, huh?"


	2. Welcome to Nimbasa

"Wow…I guess I forgot how much I missed this place."

She gazed off of the building's roof, looking around at the environment around her. The jet had landed on a heliport roof in a place called Nimbasa Town, according to her computer's map. The technology was worn on her right wrist. It looked like a customized Pokédex on the outside ( which it was), but once it was flipped open, it could be a navigational map, a computer, and lastly, a communication device with a two way feed camera. Sure, the keyboard and screen were a bit small for a computer, but it could beam out like a hologram if she needed to read something, and the keyboard flipped out, much like a sliding phone.

And of course, she was out of uniform. She wore a black tank top under a white buttoned vest, which served as a jacket. She wore hairclips to keep the sun out of her eyes with Vincent's ball dangling around her neck by a silver chain. The outfit was topped off by long dark grey jeans, a large dark navy backpack, and a pair of white and blue running shoes, caked with dirt from her adventures.

"So what do you want to do first, Vincent?" Lily asked as she stepped out onto the street, turning to face her partner whom was standing at her side. The blue-eyed Pokémon looked back at her with a small smile. "Gardevoir." He responded, pointing around them. "Ok, let's talk a walk then." The brunette agreed, understanding him.

It had really only been a few minutes of peace between the two of them as they walked around the peaceful town until they were abruptly interrupted by a loud voice.

"Hey, Lily!"

Lily halted in her tracks, turning around and smiling as she saw who was running up to her. "Oh hey Ash! What are you doing here?" She greeted, Vincent giving a shy wave. "I could say the same thing! I haven't seen you since the whole Zoroark thing!" Ash responded cheerily.

So it had been that long, huh? It wasn't completely her fault; she had been busy with 'work'. Of course Ash didn't know, and the Team Rocket Trio were too fooled by her disguise, which was really just a visor, her hair up, and a hat that she wore around them on the job.

"Ash! Where'd you go?"

Lilly looked up to see a group of three people jogging up to them. The only one she recognized was Cilan, one of the three gym leaders from Striaton City. The others were a tan skinned girl with an Axew sticking out of her dark violet-tinged hair and a brunette boy carrying a camera, followed by a Golett.

"I see you've got another troupe of traveling buddies, huh?" Lily smiled, giving a greeting wave to the new arrivals. "Oh yeah! These are my friends I made here in the Unova Region." Ash responded with a laugh, Pikachu giving a noise of agreement. "Oh, I remember you! That battle you had with Cress was an exquisite combination of strategy and cunning, a great recipe for such a battle!" Cilan beamed, shaking her hand.

After the older teen had let go of her hand, the girl stepped forward. "Hi! I'm Iris, and I'm going to be a Dragon Master!" She greeted, giving a small spin whilst her Axew gave a toothy grin from inside her hair. "Oh, a Dragon Master? Well, there's someone I want you to meet then." Lily mused, unclipping a ball from her belt and tossing it straight up. "Let's go, Aelita!"

Everyone looked up into the sky, their vision blurred by the harsh sun as a giant figure swirled down to them from above. "Oh wow! I've never seen one of these before!" Iris squealed, leaping forward to get a better look at the orange dragon. "That's because she's a Dragonite. I caught her when she was just a Dratini back in Kanto." She took a step forward, standing tall to stroke her head. "If you want to see a powerful Pokémon, look no further."

A small irritated noise from behind her caused her to turn around. "Oh, don't be like that, Vincent. You know you're _all_ superheroes to me." She gave her partner a gentle hug, one that was made easy and painless due to the irregularly small spike on his chest. Sure, the other male Gardevoir taunted him, but it let him embrace others, so it didn't bother him.

A loud yawn from Aelita made it apparent that even though she was healed, she was still tired. Lily held up her Ultra Ball for her to return inside to rest.

"Oh cool, a Gardevoir! Did you bring it over from another region too?" The brunette with the camera asked, taking a step forward. "I didn't know they could have blue eyes either!"

"It's a recessive gene. Me and Ash saw a surfing Pikachu that had blue eyes once."

"Oh yeah! I remember that!"

Lily turned back to the boy who was apparently filming her. "You must like Golett a lot, to have two of them." She smiled, looking past him to the blue duo. "Two?" He turned around to see the two Pokémon. One of them gave a laugh, giving a jump into the air before glowing brightly. When it landed back on the ground, it resembled a black and red fox.

"Oh, a Zorua! I bet you were hard to find, weren't you, little guy?" She asked, kneeling down to scratch the Pokémon behind the ears. With another snicker, the Zorua leapt up again, landing on the ground as an identical copy of herself.

"Be careful now. She likes to cause trouble." The boy laughed, taking a step forward. "Anyways, I'm Luke. I'm here to enter the Battle Competition to get material for a movie. I'm also documenting it, too."

"Oh, so that's why you're here, huh Ash? Knowing you, you probably thought this was going to be Nimbasa City." She teased, the boy's expression letting her know the answer. "Aw, shut up. So why're you here, Lily? You here for the battle competition?"

"Actually, I was just passing through. But why not? This battle competition sounds fun."

Ash gave a competitive grin. "I'm totally going to beat you this time, Lily! Just you see!"

Lily barely regarded his comment. In comparison to others, yes, he was a talented trainer. But still, he'd had Pikachu since his journey first began, and yet he still managed to make rookie mistakes, underestimate his opponents, lack follow through, and most commonly of all, took unnecessary risks that ultimately screwed him over in the end. Sometimes she wondered if he ever would become a Pokémon master. She certainly had.

"Well, let's go sign up, then!" Luke piped up, his Zorua still transformed next to her. Lily merely nodded, following them as they lead her toward a sort of building. Before they reached it though, the brunette's ears perked up. She had heard something, but what?

Her gaze turned upward, her eyes narrowing as she saw a few people standing on a rooftop. They wore dark trenchcoats, hats, and sunglasses. She recognized their body shapes, sizes, and hair color immediately.

"Oh, hey Ash? I just remembered, I still have to run by the Pokémon Center real quick. I'll catch up with you guys in a sec, ok?" Before the boy could respond, she turned and powerwalked away, cutting around the corner sharply with Vincent just behind her. Ducking into an alley, she hid in the shadows, opening the Xtransceiver function of her device. She dialed a certain frequency, adjusting an earpiece as she listened to the dial tone. The brunette remembered to slip her visor out of her backpack before a face flashed onto the screen.

"Hey, what are you three doing in Nimbasa? You're off duty." She snapped, eyes glaring from behind her visor at who answered, Jesse. "Uh, Miss Lily…! Um, we-we don't know what you're talking about!"

"Cut the act. I just saw you on a rooftop. Great disguises, by the way. The blue and magenta hair is totally convincing."

"Listen girly, we're just doing some recon! No need to be all huffy about it!" Meowth snapped back at her. "Recon for what?" James sighed; they had to answer her. She was their superior officer after all.

"We have reason to believe that there's a rare Pokémon nearby."

"Don't tell her that!" She heard Jesse whisper in the background. "Be quiet. He's following orders. Now, which Pokémon is it, James?" Lily asked, leaning against the wall behind her. "We've heard descriptions of what sounds like what might be a Zekrom."

Lily's heart skipped a beat. Last time she saw a Zekrom was….the incident at the Pokémon League….with him.

"Alright. I'll investigate as well. Stay alert." She hung up before they could say anything else, letting out a sigh. The brunette looked over at Vincent with a sort of sad expression. "Well….I guess we should join the others, huh Vince?"

The Gardevoir merely nodded, his eyes half lidded. Apparently he remembered what Zekrom meant as well. Zekrom, the legendary species of Pokémon, opposite to Reshiram._ Her_ Reshiram. A sighting of it in Unova only lead her to one conclusion.

N must be nearby.


End file.
